The invention discloses a secondary system physical loop modeling method of an intelligent substation. The secondary system physical loop modeling method of the intelligent substation includes the steps that firstly, a designer of an equipment manufacturer configures a physical loop IPCD file through a configuration tool, and a device board card and a physical end port in the IPCD file are described; secondly, a design unit solidifies the IPCD file into a cabinet model, then cable connection among cabinets and optical fiber connection among devices are designed, a substation physical loop SPCD description file is finished, and decoupling design of a logic loop and a physical loop is realized. According to the secondary system physical loop modeling and void and actuality correspondence method of the intelligent substation, an SCD file and an SPCD file correspond to each other in a void and actuality correspondence mode when a design graph is finished, void and actuality integration design description is also realized, design efficiency and accuracy are improved, many kinds of application software can be more easily developed and customized based on a solid loop model file, the engineering on-site debug method is enriched, and construction efficiency and convenience are improved.